My best guess (and those guesses tend to be pretty good)
Is maybe.. just maybe..
your hard drive is turning off..
I get this weird *click* noise in my newbie days (back in the day) and i always thought it was something wrong w/ the power supply... but anyways, getting back to the topic..
Yea, maybe its just your HD shutting off
You can control this through Windows 9x and XP by going to Start> Control Panel> Power Options> And change Turn Off Hard Disks: to whatever time seems reasonable (for me, its NEVER, because i never leave my computer idle, i suspend it or shut it down... need every penny saved on my energy bill ;-) )
But thats just my take on it.
I may be wrong.
And if i am, feel free to critisize me, it'll better prepare me for the harsh reality of... well.. reality.
Anyways, good luck,
Ed